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The US PulseNet and GenomeTrakr laboratory networks work together within the Genomics for Food Safety (Gen-FS) consortium to collect and analyze genomic data for foodborne pathogen surveillance (species include Salmonella enterica, Listeria monocytogenes, Escherichia coli (STECs), and Campylobactor). In 2017 these two laboratory networks started harmonizing their respective proficiency test exercises, agreeing on distributing a single strain-set and following the same standard operating procedure (SOP) for genomic data collection, running a jointly coordinated annual proficiency test exercise. In this data release we are publishing the reference genomes and raw data submissions for the 2017 and 2018 proficiency test exercises., Measurement(s) DNA • genome • sequence_assembly Technology Type(s) DNA sequencing • sequence assembly process Factor Type(s) species of foodborne pathogen Sample Characteristic - Organism Salmonella enterica • Escherichia coli • Listeria monocytogenes Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13135046

Outbreaks of human salmonellosis associated with live poultry contact have been reported since 1955. Multiple Salmonella serotypes have been associated with these outbreaks, and specific outbreak strains have been repeatedly linked to single hatcheries over multiple years. During 2009, four multistate outbreaks of human Salmonella infections associated with direct and indirect exposure to live poultry purchased from mail-order hatcheries and agricultural feed stores were identified, resulting in 165 culture-confirmed cases in 30 states. This report describes the epidemiologic, environmental and laboratory investigations conducted by state and local health departments, state departments of agriculture, the U.S. Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), National Poultry Improvement Plan (NPIP) and National Veterinary Services Laboratories (NVSL), and the Centers for Disease Control and Prevention (CDC). Case-patients were identified through PulseNet, the national molecular subtyping network for foodborne disease surveillance, and interviewed using the CDC standard live poultry contact questionnaire that asks about poultry-related exposures during the 7 days before illness onset. These outbreaks highlight the need to focus efforts on strategies to decrease and prevent human illness associated with live poultry contact through comprehensive interventions at the mail-order hatchery, agricultural feed store and consumer levels. Additional consumer education and interventions at mail-order hatcheries and venues where live poultry are sold, including agricultural feed stores, are necessary to prevent transmission of Salmonella from poultry to humans.

Vibrio parahaemolyticus is an aquatic halophilic bacterium that occupies estuarine and coastal marine environments, and is a leading cause of seafood-borne food poisoning cases. To investigate the environmental reservoir and potential gene flow that occurs among V. parahaemolyticus isolates, the virulence-associated gene content and genome diversity of a collection of 133 V. parahaemolyticus isolates were analyzed. Phylogenetic analysis of housekeeping genes, and pulsed-field gel electrophoresis, demonstrated that there is genetic similarity among V. parahaemolyticus clinical and environmental isolates. Whole-genome sequencing and comparative analysis of six representative V. parahaemolyticus isolates was used to identify genes that are unique to the clinical and environmental isolates examined. Comparative genomics demonstrated an O3:K6 environmental isolate, AF91, which was cultured from sediment collected in Florida in 2006, has significant genomic similarity to the post-1995 O3:K6 isolates. However, AF91 lacks the majority of the virulence-associated genes and genomic islands associated with these highly virulent post-1995 O3:K6 genomes. These findings demonstrate that although they do not contain most of the known virulence-associated regions, some V. parahaemolyticus environmental isolates exhibit significant genetic similarity to clinical isolates. This highlights the dynamic nature of the V. parahaemolyticus genome allowing them to transition between aquatic and host-pathogen states.

The presence and antimicrobial susceptibility of foodborne pathogens and indicator organisms in animal feed are not well understood. In this study, a total of 201 feed ingredient samples (animal byproducts, n=122; plant byproducts, n=79) were collected in 2002 and 2003 from representative rendering plants and the oilseed (or cereal grain) industry across the United States. The occurrence and antimicrobial susceptibility of four bacterial genera (Salmonella, Campylobacter, Escherichia coli, and Enterococcus) were determined. Salmonella isolates were further characterized by serotyping and pulsed-field gel electrophoresis (PFGE). None of the samples yielded Campylobacter or E. coli O157:H7, whereas Salmonella, generic E. coli, and Enterococcus were present in 22.9%, 39.3%, and 86.6% of samples, respectively. A large percentage (47.8%) of Salmonella-positive samples harbored two serovars, and the vast majority (88.4%) of Enterococcus isolates were E. faecium. Animal byproducts had a significantly higher Salmonella contamination rate (34.4%) than plant byproducts (5.1%) (p0.05). Among 74 Salmonella isolates recovered, 27 serovars and 55 PFGE patterns were identified; all were pan-susceptible to 17 antimicrobials tested. E. coli isolates (n=131) demonstrated similar susceptibility to these antimicrobials except for tetracycline (15.3% resistance), sulfamethoxazole (7.6%), streptomycin (4.6%), ampicillin (3.8%), and nalidixic acid (1.5%). Enterococcus isolates (n=362) were also resistant to five of 17 antimicrobials tested, ranging from 1.1% to penicillin to 14.6% to tetracycline. Resistance rates were generally higher among isolates recovered from animal byproducts. Taken together, our findings suggest that diverse populations of Salmonella, E. coli, and Enterococcus are commonly present in animal feed ingredients, but antimicrobial resistance is not common. Future large-scale studies to monitor these pathogenic and indicator organisms in feed commodities is warranted.

Salmonella enterica is recognized as one of the most common bacterial agents of foodborne illness. We report draft genomes of four Salmonella serovar Heidelberg isolates associated with the recent multistate outbreak of human Salmonella Heidelberg infections linked to kosher broiled chicken livers in the United States in 2011. Isolates 2011K-1259 and 2011K-1232 were recovered from humans, whereas 2011K-1724 and 2011K-1726 were isolated from chicken liver. Whole genome sequence analysis of these isolates provides a tool for studying the short-term evolution of these epidemic clones and can be used for characterizing potentially new virulence factors.

BACKGROUND Over 30 outbreaks of human salmonellosis linked to contact with live poultry from mail-order hatcheries were reported to Centers for Disease Control and Prevention between 1990 and 2010. In May 2009, we investigated an outbreak of human Salmonella Typhimurium infections, primarily affecting children. METHODS A case was defined as a person with the outbreak strain of Salmonella Typhimurium, as determined by pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analysis, in a Pennsylvania or New York resident with illness onset between May 1 and September 1, 2009. We conducted a case-control study to examine the relationship between illness and live poultry contact. Controls were age-matched and geographically-matched. Traceback and environmental investigations were conducted. RESULTS We identified 36 case-patients in Pennsylvania and New York; 36% were children aged ≤5 years. Case-patients were more likely than controls to report live baby poultry contact (matched odds ratio [mOR]: 17.0; 95% confidence interval [CI]: 2.7-710.5), contact with chicks (mOR: 14.0; 95% CI: 2.1-592.0), ducklings (mOR: 8.0; 95% CI: 1.1-355.0) and visiting agricultural feed stores (mOR: 6.0; 95% CI: 1.3-55.2). Most (83%) visited agricultural Feed Store Chain Y, a national agricultural feed store chain, which received poultry from Hatchery C, which is supplied by multiple egg sources. Salmonella Typhimurium was isolated from a source duck flock, but had a different pulsed-field gel electrophoresis pattern than the outbreak strain. CONCLUSIONS Live baby poultry remain an important source of human salmonellosis, particularly among children. Preventing these infections requires comprehensive interventions at hatcheries and agricultural feed stores; pediatricians should inform patients of risks associated with live poultry contact.

Vibrio parahaemolyticus is a pathogenic marine bacterium that is the main causative agent of bacterial seafood-borne gastroenteritis in the United States. An increase in the frequency of V. parahaemolyticus -related infections during the last decade has been attributed to the emergence of an O3:K6 pandemic clone in 1995. The diversity of the O3:K6 pandemic clone and its serovariants has been examined using multiple molecular techniques including multilocus sequence analysis, pulsed-field gel electrophoresis, and group-specific PCR analysis. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful tool for rapidly distinguishing between related bacterial species. In the current study, we demonstrate the development of a whole-cell MALDI-TOF MS method for the distinction of V. parahaemolyticus from other Vibrio spp. We identified 30 peaks that were present only in the spectra of the V. parahaemolyticus strains examined in this study that may be developed as MALDI-TOF MS biomarkers for identification of V. parahaemolyticus . We detected variation in the MALDI-TOF spectra of V. parahaemolyticus strains isolated from different geographical locations and at different times. The MALDI-TOF MS spectra of the V. parahaemolyticus strains examined were distinct from those of the other Vibrio species examined including the closely related V. alginolyticus , V. harveyi , and V. campbellii . The results of this study demonstrate the first use of whole-cell MALDI-TOF MS analysis for the rapid identification of V. parahaemolyticus .